ABSTRACT: In contrast to terrestrial ecology, 3D imaging technology is not well established as a method for studying species-habitat interactions in aquatic ecology. In this study we used a semi-portable, digital, 3D underwater observatory designed for long-term exposure in shallow water habitats, to assess fish-habitat interactions to artificial structures of different complexity. The observatory was mounted on a cable-car system and was moved along a 50 m transect parallel to five artificial structures of different complexity and one control site. The optical unit took high-resolution digital images, in pairs, from each structure and the control site at a frequency of 30 min over 24 hours and was then moved remotely to the next structure. The system was operated for two months without being recovered and took a total of 2160 stereoscopic image-pairs. The system proved highly valuable in assessing small-scale temporal patterns in fish-habitat interactions, as well as changes in habitat preferences of fish over the diel cycle. Such small-scale temporal and spatial patterns are most important for a detailed understanding of species-habitat interactions not only in fish but in most aquatic macro-organisms but can hardly be assessed using classical sampling devices due to labor and animal protection restrictions. However, the possibility of a significant increase in quantity of sampling through using remote imaging technology is accompanied by a significant increase in labor costs for image analysis, and therefore, further progress in semi- and fully automated systems for image analysis is needed, including 3D-imaging tools, for ecological studies.